Recent results

Jalkanen N, Trontti K, Norppa AJ, et al. INTS6 loss of function disrupts transcriptional regulation in mild intellectual disability. bioRxiv · Preprint (not peer reviewed). 10.64898/2026.07.17.737701

Budinger D, Puigdevall P, Hall GT, et al. An in vivo and in vitro spatiotemporal profile of human midbrain development. Nature Communications. 10.1038/s41467-025-67779-1

Sundaresh A, Meistermann D, Lampela R, et al. Joint profiling of cell morphology and gene expression during in vitro neurodevelopment. eLife. 10.7554/eLife.102578

Puigdevall P, Jerber J, Danecek P, Castellano S, Kilpinen H. Effects of somatic mutations on cellular differentiation in iPSC models of neurodevelopment. Cell Genomics. 10.1016/j.xgen.2023.100280

Gynter A, Meistermann D, Lähdesmäki H, Kilpinen H. DeconV: probabilistic cell type deconvolution from bulk RNA-sequencing data. bioRxiv · Preprint (not peer reviewed). 10.1101/2023.12.07.570524

Saukkonen A, Kilpinen H, Hodgkinson A. Highly accurate quantification of allelic gene expression for population and disease genetics. Genome Research. 10.1101/gr.276296.121

Bonder MJ, Smail C, Gloudemans MJ, et al. Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics. Nature Genetics. 10.1038/s41588-021-00800-7

Mirauta BA, Seaton DD, Bensaddek D, et al. Population-scale proteome variation in human induced pluripotent stem cells. eLife. 10.7554/eLife.57390

Schwartzentruber J, Foskolou S, Kilpinen H, et al. Molecular and functional variation in iPSC-derived sensory neurons. Nature Genetics. 10.1038/s41588-017-0005-8

Kilpinen H, Goncalves A, Leha A, et al. Common genetic variation drives molecular heterogeneity in human iPSCs. Nature. 10.1038/nature22403

Waszak SM, Delaneau O, Gschwind AR, et al. Population Variation and Genetic Control of Modular Chromatin Architecture in Humans. Cell. 10.1016/j.cell.2015.08.001

Waszak SM, Kilpinen H, Gschwind AR, et al. Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data. Bioinformatics. 10.1093/bioinformatics/btt667

Kilpinen H, Waszak SM, Gschwind AR, et al. Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science. 10.1126/science.1242463